4RKM | pdb_00004rkm

Wolinella succinogenes octaheme sulfite reductase MccA, form I

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.25	298	12% PEG 5000 MME, 0.1M HEPES/NaOH, 5% tacsimate pH 7.0, 4mM Zwittergent 3-12, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.121	α = 90
b = 103.042	β = 98.46
c = 233.07	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	mirrors	2014-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.381	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	49.37	100	0.199	9.2	6.6		500807	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	49.37	500807	475210	24857	99.8	0.18546	0.18546	0.18365	0.19	0.22011	0.22	RANDOM	39.25

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.64		1.45	-0.63		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.882
r_dihedral_angle_4_deg	15.005
r_dihedral_angle_3_deg	13.752
r_dihedral_angle_1_deg	5.809
r_long_range_B_refined	4.883
r_long_range_B_other	4.883
r_scangle_other	2.17
r_mcangle_it	2
r_mcangle_other	2
r_angle_refined_deg	1.309
r_scbond_it	1.267
r_scbond_other	1.267
r_mcbond_it	1.181
r_mcbond_other	1.181
r_angle_other_deg	0.776
r_chiral_restr	0.092
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	62698
Nucleic Acid Atoms
Solvent Atoms	2934
Heterogen Atoms	4382

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling